The db code is in active development at the moment, so the issue you saw with prepare being called prior to the table creation was found and fixed a little while back. I have been doing a lot of testing on the sqlite side, so I hadn't tested the mysql side recently and it had a couple other issues that had crept into the code. I just corrected these in my just-committed patch. With those changes I did some simple init/mounts/update/clean testing and it worked well.
I don't know why you're seeing an index issue with your manual table creation. The table that rsync creates works fine for me. I'm using mysql 5.5, though -- dunno if that makes a difference. Give the auto-creation a try, and if you still have issues, you might try lowering the 256 values a little to get it to fit (and tweak the code to match).
Thanks for testing, and let me know if you run into further issues.